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arguments
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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contexts
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Bugfix for GSA-647 HaplotypeCaller misses good variant because the active region doesn't trigger for an exome
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2012-11-01 15:34:04 -04:00 |
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datasources
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Replaced a useless getInt with a skipInt to remove 1/4 of the initial seek time in the BAM Index.
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2012-12-12 17:08:11 -05:00 |
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downsampling
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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examples
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Adding categories for the remaining uncategorized walkers
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2012-07-30 11:35:08 -04:00 |
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executive
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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filters
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I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).
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2012-11-27 10:26:17 -05:00 |
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io
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Don't catch a User Error and re-throw as a Reviewed Exception. That makes Eric unhappy.
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2012-11-13 11:52:47 -05:00 |
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iterators
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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phonehome
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New GATK argument interface for data and cpu threads
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2012-09-05 15:45:24 -04:00 |
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refdata
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Bug fixes to hapmap conversion in VariantsToVCF
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2012-10-29 01:45:33 -04:00 |
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report
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Bug fix for indel HMM: protect against situation where long reads (e.g. Sanger) in a pileup can lead to a read starting after the haplotype end for a given haplotype.
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2012-12-09 02:09:34 -05:00 |
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resourcemanagement
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Fixed bug in ThreadAllocation getTotalNumberOfThreads
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2012-09-05 16:35:32 -04:00 |
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samples
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Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"
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2012-09-10 15:52:39 -04:00 |
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traversals
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Add ActiveRegionReadState handling
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2012-11-28 13:59:57 -05:00 |
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walkers
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Fix for PBT bug reported on the forum: the AD is actually output correctly now (rather than with 'null' or some gibberish memory pointer).
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2012-12-13 23:28:30 +00:00 |
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CommandLineExecutable.java
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Update URL for phone home / GATK key documentation output by the GATK upon error
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2012-08-08 09:29:54 -04:00 |
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CommandLineGATK.java
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I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).
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2012-11-27 10:26:17 -05:00 |
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GenomeAnalysisEngine.java
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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ReadMetrics.java
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Mark I NanoScheduling TraverseLoci
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2012-09-05 15:45:23 -04:00 |
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ReadProperties.java
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Experimental, downsampler-friendly read shard balancer
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2012-09-21 22:17:58 -04:00 |
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WalkerManager.java
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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package-info.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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